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Yorodumi- PDB-7oy2: High resolution structure of cytochrome bd-II oxidase from E. coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oy2 | ||||||
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Title | High resolution structure of cytochrome bd-II oxidase from E. coli | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Terminal oxidase High resolution Membrane protein Membrane enzyme Oxygen reductase bd oxidase | ||||||
Function / homology | Function and homology information ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / cytochrome complex / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cell outer membrane / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.06 Å | ||||||
Authors | Grund, T.N. / Wu, D. / Bald, D. / Michel, H. / Safarian, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Mechanistic and structural diversity between cytochrome isoforms of . Authors: Tamara N Grund / Melanie Radloff / Di Wu / Hojjat G Goojani / Luca F Witte / Wiebke Jösting / Sabine Buschmann / Hannelore Müller / Isam Elamri / Sonja Welsch / Harald Schwalbe / Hartmut ...Authors: Tamara N Grund / Melanie Radloff / Di Wu / Hojjat G Goojani / Luca F Witte / Wiebke Jösting / Sabine Buschmann / Hannelore Müller / Isam Elamri / Sonja Welsch / Harald Schwalbe / Hartmut Michel / Dirk Bald / Schara Safarian / Abstract: The treatment of infectious diseases caused by multidrug-resistant pathogens is a major clinical challenge of the 21st century. The membrane-embedded respiratory cytochrome -type oxygen reductase is ...The treatment of infectious diseases caused by multidrug-resistant pathogens is a major clinical challenge of the 21st century. The membrane-embedded respiratory cytochrome -type oxygen reductase is a critical survival factor utilized by pathogenic bacteria during infection, proliferation and the transition from acute to chronic states. encodes for two cytochrome isoforms that are both involved in respiration under oxygen limited conditions. Mechanistic and structural differences between () and () operon encoded cytochrome variants have remained elusive in the past. Here, we demonstrate that cytochrome - catalyzes oxidation of benzoquinols while possessing additional specificity for naphthoquinones. Our data show that although menaquinol-1 (MK1) is not able to directly transfer electrons onto cytochrome from , it has a stimulatory effect on its oxygen reduction rate in the presence of ubiquinol-1. We further determined cryo-EM structures of cytochrome - to high resolution of 2.1 Å. Our structural insights confirm that the general architecture and substrate accessible pathways are conserved between the two oxidase isoforms, but two notable differences are apparent upon inspection: (i) does not contain a CydH-like subunit, thereby exposing heme to the membrane environment and (ii) the AppB subunit harbors a structural demethylmenaquinone-8 molecule instead of ubiquinone-8 as found in CydB of Our work completes the structural landscape of terminal respiratory oxygen reductases of and suggests that structural and functional properties of the respective oxidases are linked to quinol-pool dependent metabolic adaptations in . | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7oy2.cif.gz | 177.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oy2.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 7oy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oy2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7oy2_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7oy2_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 7oy2_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oy2 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oy2 | HTTPS FTP |
-Related structure data
Related structure data | 13108MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytochrome bd-II ubiquinol oxidase subunit ... , 2 types, 2 molecules BC
#1: Protein | Mass: 42448.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: appB, cbdB, cyxB, b0979, JW0961 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): CLY References: UniProt: P26458, ubiquinol oxidase (H+-transporting) |
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#2: Protein | Mass: 57962.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: appC, cbdA, cyxA, b0978, JW0960 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): CLY References: UniProt: P26459, ubiquinol oxidase (H+-transporting) |
-Protein , 1 types, 1 molecules X
#3: Protein | Mass: 6436.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: appX, yccB, b4592, JW0961.1, b0979.1 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): CLY / References: UniProt: P24244 |
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-Non-polymers , 7 types, 31 molecules
#4: Chemical | ChemComp-CDN / | ||||||
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#5: Chemical | ChemComp-DK8 / | ||||||
#6: Chemical | ChemComp-POV / ( | ||||||
#7: Chemical | #8: Chemical | ChemComp-HDD / | #9: Chemical | ChemComp-OXY / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cytochrome bd-II oxidase from E. coli composed of subunit AppB, AppC and AppX Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.104 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (strain K12) (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 108 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 533309 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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